I'd like to use the RNA-seq data from CCLE found at https://portals.broadinstitute.org/ccle/data. Where may I find more information about the methods that were considered to process the data?
Thanks in advance
rf
•
written
by
fr
1 answer
E ai cara, check the original publication: The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity
In particular, look at Supplementary Material 1 (Word doc) - it has information on each of the following:
Supplementary Methods
1. Cell line selection and annotation
2. DNA and RNA extraction
3. Genomic characterization
SNP Arrays:
DNA identity analysis by mass spectrometric SNP genotyping
4. Cell line identity validation by SNP genotyping
5. Gene set activity scores
6. Cell line-to-primary tumor comparison
Copy-number comparison:
Expression comparison:
Mutation-rate comparison
7. Pharmacological characterization
8. Prediction of drug response
8.1. Sensitivity prediction using regression analysis
8.2. Sensitivity prediction using categorical analysis
9. AHR validation experiments
Cell lines and cell culture conditions
Lentivirally delivered short hairpin RNA
Immunoblot analysis:
Analysis of mRNA expression by quantitative RT-PCR (qRT-PCR)
Growth curves
Pharmacologic growth inhibition curves
10. Data sharing/release
All raw and processed data are available at the CCLE website: www.broadinstitute.org/ccle In addition, the website offers direct links to data visualization tools such as IGV39, as well as genepattern-based40 analysis tools for expression and copy-number class comparison analyses.
Take a look here: CCLE RNA-seq library protocol
De nada amigo.
Where can I find information on how they analyzed the RNA-seq data? Thank you!
Read the supplementary material.
Thanks, Kevin. Just for an updated reference, I found the RNA-seq analysis info as part of this paper: Next-generation characterization of the Cancer Cell Line Encyclopedia
Hello my friend. Where have you looked already? The CCLE ma not report the PAM50 subtypes.
I have seen that it is reported in this paper [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001206/#MOESM1] But it is based on microarray data. What I need is for RNAseq data.
I see, but those authors appear to have done the work on their own. That is, you extract the PAM50 genes from the data and then perform some clustering analysis in order to see how your samples are grouped based on the PAM50 genes. PAM50 is just a list of genes, after all. One can explore the utility of the signature in any expression dataset.
If you just need to know the genes, then take a look here: Where To Download Pam50 Gene Set?
Log in to answer this question.
-
Multiple annotation in my table counts
written by omicon •
-
Finding Mutations in CCLE Samples
written by mbabolda •
-
CCLE miRNA expression data
written by baris.blknt •
-
Can be merged biological replicates?
written by star
-
Where to find CCLE metadata?
written by fr
-
alignment used for CCLE RNA-seq
written by Amos •
-
Drug database for cell line experiments with before vs after treatment responses
written by fr
-
Accessing legacy data in GDC
written by fr
-
Cell Line (SUM225 and MCF0) RNA Seq data
written by bioinformatics.cancer
-
CCLE RNA-seq library protocol
written by zju.whw •
